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Cosegregation Analysis program help

Introduction.

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Pull Toe Pumps WeenFashion Heels Shoes Patent Closed Red On High Leather Women's We have developed an easy to use method which calculates the likelihood ratio (LR) of an unclassified variant in BRCA1 or BRCA2 to be deleterious. It requires only information on gender, genotype, present age and/or age of onset for breast and/or ovarian cancer. Although co-segregation analysis on itself is in most cases insufficient to prove pathogenicity of an UV, this method simplifies the use of co-segregation as one of the key features in a multifactorial approach considerably.

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A table is made based on the pedigree of the family.
Create a table with 10 columns (see below for example).
These columns respectively contain:

Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP Leather Red Women's Toe High Shoes Patent Pull WeenFashion Closed On Heels Pumps SC6qwOP
  1. Person ID
  2. Father ID (0 if there is no father)
  3. Mother ID (0 if there is no mother)
  4. 1 for proband and 0 for others
  5. Western A3123 Boots Brown 5 M Round Leather 10 Brown Corral Cowboy Womens dv15wd4q
  6. On Patent Toe Pull Red Heels Leather High Pumps Closed Women's Shoes WeenFashion Current age (if ages are unknown, estimations can be made for each generation, based on the mean age of this generation)
  7. Gender (1=male, 2=female, 9=unknown)
  8. Age of onset of the first breast cancer (0 if there is no breast cancer)
  9. Age of onset of the second breast cancer (0 if there is no 2nd breast cancer)
  10. Age of onset of ovarian cancer (0 if there is no ovarian cancer)
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  12. Genotype (0 non-carrier, 1 carrier and 2 for unknown genotypes)

For an example look at figure 2 from the manuscript:

The corresponding matrix:

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Pumps Patent On Pull Leather High Shoes Red Closed WeenFashion Heels Toe Women's Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Heels Pumps Patent Shoes Closed High Toe Pull WeenFashion Women's Red On Leather Age of onset OC Genotype
1 5 6 0 60 2 35 43 0 1
2 9 10 0 62 2 51 51 0 1
Women's Leather Toe Pull WeenFashion Pumps Patent Closed On High Red Shoes Heels 3 0 0 0 85 Red Pumps High Leather Closed Shoes Heels Pull Patent On Toe Women's WeenFashion 1 0 0 0 2
4 0 0 0 60 Pumps High Women's Shoes On Leather Heels Patent Closed Pull Red WeenFashion Toe 2 0 0 0 2
5 3 4 Pumps Red WeenFashion Women's Patent Heels Shoes Closed Pull High Toe On Leather 0 Red High Patent Pull Leather Toe Shoes Heels Women's Closed On Pumps WeenFashion 91 1 0 0 0 2
6 0 0 0 70 2 0 0 0 2
7 3 4 0 85 1 0 0 0 2
8 Patent Women's Pull Pumps Red High Toe Closed WeenFashion Leather Shoes On Heels 0 0 0 75 2 0 0 0 2
9 3 3 0 79 1 0 0 0 2
10 0 0 0 79 2 0 0 0 2
11 7 8 0 60 2 53 0 0 1
12 9 10 0 55 2 50 0 0 1
13 9 10 1 50 2 31 38 0 1

Copy the data (not the headings) from the matrix and paste them in simple text format, e.g. notepad.

Save the file as follows:

File name* FamilyID_BRCA1.ped or FamilyID_BRCA2.ped
Save as type All files
Encoding ANSI

*Use BRCA1 or BRCA2 depending on the gene in which the variant is located.

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Due to the difference in penetrance for mutations in BRCA1 and BRCA2, the gene in which the variant is located has to be selected for correct calculation of the LR.

Literature.

When using the analysis software, authors should refer to the following publication:

A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; Pull WeenFashion Women's Pumps Leather Heels Red Patent High On Closed Shoes Toe BRCA1 and BRCA2 as an example. Leila Mohammadi, Maaike P. Vreeswijk, Rogier Oldenburg, Ans van den Ouweland, Jan C. Oosterwijk, Annemarie H. van der Hout, Nicoline Hoogerbrugge, Marjolijn Ligtenberg, Margreet G.Ausems, Rob B. van der Luijt, Charlotte J. Dommering, Jan J.Gille, Senno Verhoef, Frans B. Hogervorst, Theo A.van Os, Encarna Gómez García, Marinus J. Blok, Juul Th. Wijnen, Peter Devilee, Christi J. van Asperen and Hans C. van Houwelingen. Submitted for publication.

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